Expectation Maximization Research Articles

Knowledge discovery of patients reviews on breast cancer drugs: Segmentation of side effects using machine learning techniques

Breast cancer stands as the most frequently diagnosed life-threatening cancer among women worldwide. Understanding patients' drug experiences is essential to improving treatment strategies and outcomes. In this research, we conduct knowledge discovery on breast cancer drugs using patients' reviews. A new machine learning approach is developed by employing clustering, text mining and regression techniques. We first use Latent Dirichlet Allocation (LDA) technique to discover the main aspects of patients' experiences from the patients' reviews on breast cancer drugs. We also use Expectation-Maximization (EM) algorithm to segment the data based on patients' overall satisfaction. We then use the Forward Entry Regression technique to find the relationship between aspects of patients' experiences and drug's effectiveness in each segment. The textual reviews analysis on breast cancer drugs found 8 main side effects: Musculoskeletal Effects, Menopausal Effects, Dermatological Effects, Metabolic Effects, Gastrointestinal Effects, Neurological and Cognitive Effects, Respiratory Effects and Cardiovascular. The results are provided and discussed. The findings of this study are expected to offer valuable insights and practical guidance for prospective patients, aiding them in making informed decisions regarding breast cancer drug consumption.

Accuracy of holmium-166 SPECT/CT quantification over a large range of activities

BackgroundQuantitative imaging is a crucial step for dosimetry in radionuclide therapies. Traditionally, SPECT/CT imaging is quantified based on scanner-specific conversion factors or self-calibration, but recently absolute quantification methods have been introduced in commercial SPECT reconstruction software (Broad Quantification, Siemens Healthineers). In this phantom study we investigate the accuracy of three quantification methods for holmium-166 SPECT/CT imaging, and provide recommendations for clinical dosimetry.MethodsOne cylindrical phantom, filled with a homogeneous holmium-166-chloride activity concentration solution, was imaged at one time point to determine a scanner-specific conversion factor, and to characterize the spatial dependency of the activity concentration recovery. One Jaszczak phantom with six fillable spheres, 10:1 sphere-to-background ratio, was imaged over a large range of holmium-166 activities (61-3130 MBq). The images were reconstructed with either an ordered subset expectation maximization (OSEM, Flash3D-reconstruction; scanner-specific quantification or self-calibration quantification) or an ordered subset conjugate gradient (OSCG, xSPECT-reconstruction; Broad Quantification) algorithm. These three quantification methods were compared for the data of the Jaszczak phantom and evaluated based on whole phantom recovered activity, activity concentration recovery coefficients (ACRC), and recovery curves.ResultsThe activity recovery in the Jaszczak phantom was 28–115% for the scanner-specific, and 57–97% for the Broad Quantification quantification methods, respectively. The self-calibration-based activity recovery is inherently always 100%. The ACRC for the largest sphere (Ø60 mm, ~ 113 mL) ranged over (depending on the activity level) 0.22–0.89, 0.76–0.86, 0.39–0.72 for scanner-specific, self-calibration and Broad Quantification, respectively.ConclusionOf the three investigated quantification methods, the self-calibration technique produces quantitative SPECT images with the highest accuracy in the investigated holmium-166 activity range.

Statistical inference of Poisson censored δ-shock model

In this article, the sufficient statistics, complete statistics, and a uniformly minimum variance unbiased estimate (UMVUE) of the failure parameters of the Poisson censored δ -shock model are obtained, which are based on the sample data of shock arrival time. The maximum likelihood estimates of the shock parameters are also obtained by using the EM algorithm, which is based on the total number of observed shock samples. Finally, the estimation errors and convergence rate of the EM iteration are simulated numerically using Matlab R2016b.

A 3D imaging system for dosimetry in FLASH radiotherapy

This study examines the feasibility of reconstructing the spatial dose distribution delivered by a 9 MeV electron beam within a plastic scintillator block using optical tomography. The system is designed for use in 3D-dosimetry for clinical applications in quality assurance and beam characterization, especially with FLASH-beam sources. The proposed detector reconstructs the 3D dose distribution map employing a monolith with 10 cm side, imaged in four different projections by scientific cameras. The 3D dose distribution simulated with Geant4 was reconstructed using a maximum likelihood expectation maximization algorithm applied to the lateral projection, resulting in a longitudinal image with a standard deviation of 0.2 Gy. Furthermore, a preliminary experimental test has been performed.

A Highly Efficient Compressive Sensing Algorithm Based on Root-Sparse Bayesian Learning for RFPA Radar

Off-grid issues and high computational complexity are two major challenges faced by sparse Bayesian learning (SBL)-based compressive sensing (CS) algorithms used for random frequency pulse interval agile (RFPA) radar. Therefore, this paper proposes an off-grid CS algorithm for RFPA radar based on Root-SBL to address these issues. To effectively cope with off-grid issues, this paper derives a root-solving formula inspired by the Root-SBL algorithm for velocity parameters applicable to RFPA radar, thus enabling the proposed algorithm to directly solve the velocity parameters of targets during the fine search stage. Meanwhile, to ensure computational feasibility, the proposed algorithm utilizes a simple single-level hierarchical prior distribution model and employs the derived root-solving formula to avoid the refinement of velocity grids. Moreover, during the fine search stage, the proposed algorithm combines the fixed-point strategy with the Expectation-Maximization algorithm to update the hyperparameters, further reducing computational complexity. In terms of implementation, the proposed algorithm updates hyperparameters based on the single-level prior distribution to approximate values for the range and velocity parameters during the coarse search stage. Subsequently, in the fine search stage, the proposed algorithm performs a grid search only in the range dimension and uses the derived root-solving formula to directly solve for the target velocity parameters. Simulation results demonstrate that the proposed algorithm maintains low computational complexity while exhibiting stable performance for parameter estimation in various multi-target off-grid scenarios.

Improving community detection in blockmodel by distance-based observation selection

Community detection is an important research topic in complex systems and has plenty of applications in real-world networks. Probabilistic methods, such as the Expectation–Maximization (EM), are developed to classify nodes that have similar connection patterns in a network based on blockmodels. However, the detection procedures in these models are typically started from randomly generated initial community distributions without prior knowledge. In biological and social networks, there are practical measures to obtain prior knowledge for a subset of nodes, such as local observations. These facts lead us to question how we can select a subset of nodes with known community labels to enhance the accuracy of the EM method. The current selection methods lack the relationship between detection accuracy and structural characteristics and most approaches consider the nodes as the center of communities, which is not suitable for block models. In this paper, we first study the relationships between the structural distance and detection accuracy without prior knowledge. Then we propose a distance-based indicator to describe the performance of the observation node set in the EM method. Finally, we introduce a scoring method based on the indicator to select a partial observation set, improving the accuracy of community detection using the EM method. Empirical results from synthetic and real-world networks corroborate that the proposed indicator could contribute to a better performance in kinds of scenarios.

Short-term prediction of horizontal winds in the mesosphere and lower thermosphere over coastal Peru using a hybrid model

The mesosphere and lower thermosphere (MLT) are transitional regions between the lower and upper atmosphere. The MLT dynamics can be investigated using wind measurements conducted with meteor radars. Predicting MLT winds could help forecast ionospheric parameters, which has many implications for global communications and geo-location applications. Several literature sources have developed and compared predictive models for wind speed estimation. However, in recent years, hybrid models have been developed that significantly improve the accuracy of the estimates. These integrate time series decomposition and machine learning techniques to achieve more accurate short-term predictions. This research evaluates a hybrid model that is capable of making a short-term prediction of the horizontal winds between 80 and 95 km altitudes on the coast of Peru at two locations: Lima (12°S, 77°W) and Piura (5°S, 80°W). The model takes a window of 56 data points as input (corresponding to 7 days) and predicts 16 data points as output (corresponding to 2 days). First, the missing data problem was analyzed using the Expectation Maximization algorithm (EM). Then, variational mode decomposition (VMD) separates the components that dominate the winds. Each resulting component is processed separately in a Long short-term memory (LSTM) neural network whose hyperparameters were optimized using the Optuna tool. Then, the final prediction is the sum of the predicted components. The efficiency of the hybrid model is evaluated at different altitudes using the root mean square error (RMSE) and Spearman’s correlation (r). The hybrid model performed better compared to two other models: the persistence model and the dominant harmonics model. The RMSE ranged from 10.79 to 27.04 m s−1, and the correlation ranged from 0.55 to 0.94. In addition, it is observed that the prediction quality decreases as the prediction time increases. The RMSE at the first step reached 6.04 m s−1 with a correlation of 0.99, while at the sixteenth step, the RMSE increased up to 30.84 m s−1 with a correlation of 0.5.

Unsupervised machine learning with different sampling strategies and topographic factors for distinguishing between landslide source and runout areas to improve landslide inventory production

This study derived 12 topographical and hydrological factors related to landslides from a 10-m digital elevation model. Three unsupervised machine learning algorithms were employed to distinguish between the features of landslide sources and runout areas for Typhoon Morakot. Two sampling strategies were designed in this study. The first strategy involved creating a data set by pairing landslide sources and runout areas on the basis of the size of polygonal areas recorded in the inventory and then exploring the effectiveness of feature separation with k-means++ as the primary method and EM (expectation maximization) and DBSCAN (Density-Based Spatial Clustering of Applications with Noise) as supplementary methods. Because of practical challenges associated with the inability to determine whether remote sensing results correspond to landslide sources or runout areas, the first sampling strategy was used to test the feasibility of the adopted algorithms. In the second sampling strategy, the effectiveness of feature separation was tested by dividing polygon samples into several intervals on the basis of their sizes, thereby verifying the practicability of the adopted algorithms in real-world operations. This study verified that combining unsupervised machine learning algorithms with topographic factors facilitates the effective separation of landslide sources and runout areas, thereby enhancing the quality of landslide inventories and reducing the cost of landslide inventory creation. Moreover, it indicated that meter-scale topographic data yield classification results similar to those obtained from manually created landslide inventories based on centimeter-scale stereo aerial photos. The proposed method effectively balances the cost and quality of landslide inventories.

Novel Adaptive Hidden Markov Model Utilizing Expectation–Maximization Algorithm for Advanced Pipeline Leak Detection

Novel Adaptive Hidden Markov Model Utilizing Expectation–Maximization Algorithm for Advanced Pipeline Leak Detection

TIPS: a novel pathway-guided joint model for transcriptome-wide association studies.

In the past two decades, genome-wide association studies (GWAS) have pinpointed numerous SNPs linked to human diseases and traits, yet many of these SNPs are in non-coding regions and hard to interpret. Transcriptome-wide association studies (TWAS) integrate GWAS and expression reference panels to identify the associations at gene level with tissue specificity, potentially improving the interpretability. However, the list of individual genes identified from univariate TWAS contains little unifying biological theme, leaving the underlying mechanisms largely elusive. In this paper, we propose a novel multivariate TWAS method that Incorporates Pathway or gene Set information, namely TIPS, to identify genes and pathways most associated with complex polygenic traits. We jointly modeled the imputation and association steps in TWAS, incorporated a sparse group lasso penalty in the model to induce selection at both gene and pathway levels and developed an expectation-maximization algorithm to estimate the parameters for the penalized likelihood. We applied our method to three different complex traits: systolic and diastolic blood pressure, as well as a brain aging biomarker white matter brain age gap in UK Biobank and identified critical biologically relevant pathways and genes associated with these traits. These pathways cannot be detected by traditional univariate TWAS + pathway enrichment analysis approach, showing the power of our model. We also conducted comprehensive simulations with varying heritability levels and genetic architectures and showed our method outperformed other established TWAS methods in feature selection, statistical power, and prediction. The R package that implements TIPS is available at https://github.com/nwang123/TIPS.

Applying the Expectation-Maximization Algorithm to Multivariate Signal Extraction

Understanding time series signal extraction is vital for federal agencies, especially as data collection accelerates. One natural extension is moving from univariate to multivariate signal extraction, which offers the promise of reducing extraction error by exploiting cross-sectional relationships. However, such an extension ushers in new computational challenges, viz. larger parameter spaces and more complicated objective functions. The Expectation-Maximization (EM) algorithm provides a methodology to implicitly compute (or approximate) maximum likelihood estimates (MLEs). This paper provides methodology for applying the EM algorithm to a class of latent component multivariate time series models that allow for a nuanced specification of the unobserved signal. We derive an explicit formula for the maximization step, which facilitates computation speed while also improving the stability of the algorithm. Numerical studies demonstrate EM’s ability to efficiently compute MLEs in low-dimensional systems, while also providing feasible estimates in moderate-dimensional systems where MLEs are infeasible to compute. Applications to monthly housing starts and daily immigration are provided.

Accelerated distributed expectation-maximization algorithms for the parameter estimation in multivariate Gaussian mixture models

Rapid development for modeling big data requires effective and efficient methods for estimating the parameters involved. Although several accelerated Expectation-Maximization algorithms have been developed, there still exist two major concerns: reducing computational cost and improving model estimation accuracy. We propose three distributed-like algorithms for multivariate Gaussian mixture models, which can accelerate speed and improve estimation accuracy. The first algorithm is distributed algorithm, which is used to speed up the calculation of classic algorithms and improve its estimation accuracy by averaging the one-step estimators obtained from distributed operators. The second algorithm is distributed online algorithm, which is a distributed stochastic approximation procedure that performs online updates when reading online data. The final algorithm is called distributed monotonically over-relaxed algorithm, which uses an over-relaxation factor and a distributing strategy to improve the estimation accuracy of multivariate Gaussian mixture models. We investigate the stability, sensitivity, convergence, and robustness of these algorithms in a numerical study. We also apply these algorithms to three real data sets for validation.

Estimation and Bayesian Prediction of the Generalized Pareto Distribution in the Context of a Progressive Type-II Censoring Scheme

The generalized Pareto distribution plays a significant role in reliability research. This study concentrates on the statistical inference of the generalized Pareto distribution utilizing progressively Type-II censored data. Estimations are performed using maximum likelihood estimation through the expectation–maximization approach. Confidence intervals are derived using the asymptotic confidence intervals. Bayesian estimations are conducted using the Tierney and Kadane method alongside the Metropolis–Hastings algorithm, and the highest posterior density credible interval estimation is accomplished. Furthermore, Bayesian predictive intervals and future sample estimations are explored. To illustrate these inference techniques, a simulation and practical example are presented for analysis.

The potential of mixing model of wind speed distribution in Algerian High Plateaus

The evaluation of wind energy relies primarily on the probability density function PDF, which corresponds well with the wind speed data. Single PDFs are widely used in the assessment of wind. In contrast, homogeneous or heterogeneous mixed models are rarely used, especially in Algeria, where the bimodal wind speed distribution is expected. This research aims to investigate the potential of heterogeneous PDFs Generalized Extreme Value-Weibul and Normal-Extreme Value PDFs in assessing wind energy at three meteorological stations in the high plateau against the single widespread PDFs Weibull and GEV by analyzing five years of archived wind speed data. The estimation of mixed model parameters is obtained by applying the Expectation-Maximization algorithm, and the identification of the appropriate PDF is obtained by four goodness-of-fit (GOF) criteria and compared with the widespread single distributions. The results show that the mixed model surpasses widely the single model for all the GOF criteria used at the three selected sites. The proposed mixed model fits all the wind speed distributions related to unimodal and bimodal regimes.

Height-Resolved Analysis of Indoor Airborne Microbiome: Comparison with Floor Dust-Borne Microbiome and the Significance of Shoe Sole Dust.

Exposure to the indoor airborne microbiome is closely related to the air that individuals breathe. However, the floor dust-borne microbiome is commonly used as a proxy for indoor airborne microbiome, and the spatial distribution of indoor airborne microbiome is less well understood. This study aimed to characterize indoor airborne microorganisms at varying heights and compare them with those in floor dust. An assembly of three horizontally and three vertically positioned Petri dishes coated with mineral oil was applied for passive air sampling continuously at three heights without interruption. The airborne microbiomes at the three different heights showed slight stratification and differed significantly from those found in the floor dust. Based on the apportionment results from the fast expectation-maximization algorithm (FEAST), shoe sole dust contributed approximately 4% to indoor airborne bacteria and 14% to airborne fungi, a contribution that is comparable to that from the floor dust-borne microbiome. The results indicated that floor dust may not be a reliable proxy for indoor airborne microbiome. Moreover, the study highlights the need for height-resolved studies of indoor airborne microbiomes among humans in different activity modes and life states. Additionally, shoe sole-dust-associated microorganisms could potentially be a source to "re-wild" the indoor microbiota.

Prevalence estimates for COVID-19-related health behaviors based on the cheating detection triangular model

BackgroundSurvey studies in medical and health sciences predominantly apply a conventional direct questioning (DQ) format to gather private and highly personal information. If the topic under investigation is sensitive or even stigmatizing, such as COVID-19-related health behaviors and adherence to non-pharmaceutical interventions in general, DQ surveys can lead to nonresponse and untruthful answers due to the influence of social desirability bias (SDB). These effects seriously threaten the validity of the results obtained, potentially leading to distorted prevalence estimates for behaviors for which the prevalence in the population is unknown. While this issue cannot be completely avoided, indirect questioning techniques (IQTs) offer a means to mitigate the harmful influence of SDB by guaranteeing the confidentiality of individual responses. The present study aims at assessing the validity of a recently proposed IQT, the Cheating Detection Triangular Model (CDTRM), in estimating the prevalence of COVID-19-related health behaviors while accounting for cheaters who disregard the instructions.MethodsIn an online survey of 1,714 participants in Taiwan, we obtained CDTRM prevalence estimates via an Expectation-Maximization algorithm for three COVID-19-related health behaviors with different levels of sensitivity. The CDTRM estimates were compared to DQ estimates and to available official statistics provided by the Taiwan Centers for Disease Control. Additionally, the CDTRM allowed us to estimate the share of cheaters who disregarded the instructions and adjust the prevalence estimates for the COVID-19-related health behaviors accordingly.ResultsFor a behavior with low sensitivity, CDTRM and DQ estimates were expectedly comparable and in line with official statistics. However, for behaviors with medium and high sensitivity, CDTRM estimates were higher and thus presumably more valid than DQ estimates. Analogously, the estimated cheating rate increased with higher sensitivity of the behavior under study.ConclusionsOur findings strongly support the assumption that the CDTRM successfully controlled for the validity-threatening influence of SDB in a survey on three COVID-19-related health behaviors. Consequently, the CDTRM appears to be a promising technique to increase estimation validity compared to conventional DQ for health-related behaviors, and sensitive attributes in general, for which a strong influence of SDB is to be expected.

Dynamic mode decomposition based on expectation–maximization algorithm for simultaneous system identification and denoising

The present study proposes a novel dynamic mode decomposition (DMD) that can simultaneously estimate the reduced-order model, the original signal, and the system/observation noise model only from the noisy data. An expectation–maximization (EM)-algorithm DMD (EMDMD) combines DMD and the parameter adjustment of the linear dynamical system (LDS) based on the EM algorithm. The initial parameters based on the linearity of the reduced-order data are set by using DMD. Subsequently, the log-likelihood of the complete data is maximized by adjusting the LDS parameters while separating the noise. The proposed algorithm is applied to the benchmark data of the short-fat and tall-skinny data matrices with different noise and the time-series velocity fields of the flow around a circular cylinder and the separated flow around an airfoil. The performance of EMDMD in terms of system identification and noise separation from the noisy data is evaluated, and the EMDMD shows the highest system identification and noise separation performance in all data.

An Expectation-Maximization framework for Personalized Itinerary Recommendation with POI Categories and Must-see POIs

In this paper, we introduce a novel deterministic method based on Expectation Maximization (EM) to solve the rather complex problem of designing a tourist trip or Personalized Itinerary Recommendation (PIR). PIR objective is to recommend a personalized tour consisting of successive Points of Interest (POIs), which maximizes user satisfaction and respects user time-frame constraints. On top of that, the POIs are divided into categories, in order for travelers to be able to set limits on the maximum (and minimum) number of POIs that belong to one category and are included in the itinerary. In the proposed framework, emphasis is given on the POIs sequence selection, which exploits the customized POI recommendations offered by a recommender system. Additionally, the proposed methodology with POIs categories is able to solve the TourMustSee problem, so that the tour includes a set of POIs that must be visited. The proposed system has been successfully incorporated into a mobile app, offering a complete tourist trip design. The high performance, resilience, and computational efficiency of the proposed framework are demonstrated by experimental findings and comparisons to existing approaches on numerous synthetic and real datasets.

HCMV detection in Asian gastric cancer RNA-seq data sets and clinical validation in Indian GC patients reveals the HCMV-GC specific gene signatures.

Gastric cancer (GC) prevalence is very high in the Asian population. Oncogenic viruses play a crucial role in the progression of different types of cancers. Through reanalysis of clinical RNA-seq data sets derived from Asian GC patients, this study identified the presence of human cytomegalovirus (HCMV) in Asian GC tumors, next to the well-studied association of EBV. Clinical recruitment of the Indian GC cohort and screening for HCMV presence identified a 14.28% occurrence, similar to that observed in the bioinformatics analysis. A combinatorial approach of rank-based meta-analysis and ranking of groups based on an expectation-maximization algorithm identified that the upregulated LINC02864 and MAGEA10 correlated with poor survival of GC patients and downregulated tumor suppressor genes enriching for gastric acid secretion pathway to be associated with HCMV-positive GC patients, revealing the progressive role of HCMV infection in GC. Genes that discriminate between different stages of GC were identified through feature selection implemented in a machine-learning approach. LTF and KLK10 expressions were found to be specifically dysregulated by HCMV and can also indicate the GC stages. The results of this study will guide future studies to identify the functional role of these genes in the HCMV-associated GC.IMPORTANCENearly 75% of gastric cancer (GC) cases reported globally are from the Asian population. Most existing public databases, such as TCGA, comprise only a fractional portion of data derived from Asian ancestry. This study identified EBV and human cytomegalovirus (HCMV)'s higher detection in GC patients. The presence and role of EBV associated with GC are well-known, and the observation of HCMV prompted us to validate the findings in a small cohort of 40 Indian GC patients. We observed a 14.28% occurrence of HCMV in the Indian cohort, similar to that observed from next-generation sequencing. A combinatorial approach of rank-based meta-analysis and ranking of groups based on an expectation-maximization algorithm identified that the upregulated LINC02864 and MAGEA10 correlated with poor survival of GC patients and downregulated tumor suppressor genes enriching for gastric acid secretion pathway to be associated with HCMV-positive GC patients, revealing the progressive role of HCMV infection in GC.

Predicting demand for new products in fashion retailing using censored data

In today’s highly competitive fashion retail market, it is crucial to have accurate demand forecasting systems, namely for new products. Many experts have used machine learning techniques to forecast product sales. However, sales that do not happen due to lack of product availability are often ignored, resulting in censored demand and service levels that are lower than expected. Motivated by the relevance of this issue, we developed a two-stage approach to forecast the demand for new products in the fashion retail industry. In the first stage, we compared four methods of transforming historical sales into historical demand for products already commercialized. Three methods used sales-weighted averages to estimate demand on the days with stock-outs, while the fourth method employed an Expectation-Maximization (EM) algorithm to account for potential substitute products affected by stock-outs of preferred products. We then evaluated the performance of these methods and selected the most accurate one for calculating the primary demand for these historical products. In the second stage, we predicted the demand for the products of the following collection using Random Forest, Deep Neural Networks, and Support Vector Regression algorithms. In addition, we applied a model that consisted of weighting the demands previously calculated for the products of past collections that were most similar to the new products. We validated the proposed methodology using a European fashion retailer case study. The results revealed that the method using the Expectation-Maximization algorithm had the highest potential, followed by the Random Forest algorithm. We believe that this approach will lead to more assertive and better-aligned decisions in production management.